Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 15:18:34 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fdg_31542/12_2021/7fdg_31542.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fdg_31542/12_2021/7fdg_31542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fdg_31542/12_2021/7fdg_31542.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fdg_31542/12_2021/7fdg_31542.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fdg_31542/12_2021/7fdg_31542.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fdg_31542/12_2021/7fdg_31542.pdb" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.724 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 23": "OE1" <-> "OE2" Residue "A PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 37": "OE1" <-> "OE2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 115": "NH1" <-> "NH2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "A GLU 145": "OE1" <-> "OE2" Residue "A ASP 157": "OD1" <-> "OD2" Residue "A TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 160": "OE1" <-> "OE2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "A TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 206": "OD1" <-> "OD2" Residue "A TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 213": "OD1" <-> "OD2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A ASP 225": "OD1" <-> "OD2" Residue "A ARG 245": "NH1" <-> "NH2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ASP 382": "OD1" <-> "OD2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 430": "OE1" <-> "OE2" Residue "A ASP 431": "OD1" <-> "OD2" Residue "A PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A GLU 479": "OE1" <-> "OE2" Residue "A GLU 489": "OE1" <-> "OE2" Residue "A PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 518": "NH1" <-> "NH2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "A GLU 549": "OE1" <-> "OE2" Residue "A PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 571": "OE1" <-> "OE2" Residue "A GLU 589": "OE1" <-> "OE2" Residue "A TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 615": "OD1" <-> "OD2" Residue "E PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 357": "NH1" <-> "NH2" Residue "E TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 398": "OD1" <-> "OD2" Residue "E GLU 406": "OE1" <-> "OE2" Residue "E ASP 420": "OD1" <-> "OD2" Residue "E GLU 484": "OE1" <-> "OE2" Residue "E PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 516": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/chem_data/mon_lib" Total number of atoms: 6459 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4847 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 597, 4840 Classifications: {'peptide': 597} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 26, 'TRANS': 569, 'PCIS': 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Conformer: "B" Number of residues, atoms: 597, 4840 Classifications: {'peptide': 597} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 26, 'TRANS': 569, 'PCIS': 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 bond proxies already assigned to first conformer: 4968 Chain: "E" Number of atoms: 1542 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 183} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 183} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 1573 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.03, per 1000 atoms: 1.09 Number of scatterers: 6459 At special positions: 0 Unit cell: (116.48, 87.36, 80.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 35 16.00 O 1227 8.00 N 1063 7.00 C 4134 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.04 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.02 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.04 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.04 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.02 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amimo acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 701 " - " ASN A 322 " " NAG A 702 " - " ASN A 53 " " NAG A 703 " - " ASN A 546 " " NAG A 704 " - " ASN A 90 " " NAG E 601 " - " ASN E 343 " Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 1.8 seconds 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1492 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 6 sheets defined 56.9% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.896A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN A 53 " --> pdb=" O ASN A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.641A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 146 through 154 Processing helix chain 'A' and resid 157 through 172 removed outlier: 4.149A pdb=" N VAL A 172 " --> pdb=" O TRP A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 194 Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 218 through 252 Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 275 through 282 removed outlier: 3.689A pdb=" N TYR A 279 " --> pdb=" O TRP A 275 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER A 280 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.786A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 413 removed outlier: 4.031A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 removed outlier: 3.616A pdb=" N ILE A 421 " --> pdb=" O HIS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 447 Processing helix chain 'A' and resid 448 through 465 removed outlier: 3.993A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.700A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.332A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.601A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.672A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 364 through 371 removed outlier: 4.216A pdb=" N LEU E 368 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.004A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 421 Processing helix chain 'E' and resid 438 through 443 removed outlier: 3.903A pdb=" N SER E 443 " --> pdb=" O ASN E 439 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.709A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 5.659A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.850A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'E' and resid 473 through 474 removed outlier: 3.652A pdb=" N TYR E 473 " --> pdb=" O TYR E 489 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYR E 489 " --> pdb=" O TYR E 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 322 hydrogen bonds defined for protein. 916 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.74 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2068 1.35 - 1.47: 1800 1.47 - 1.60: 2721 1.60 - 1.72: 0 1.72 - 1.85: 54 Bond restraints: 6643 Sorted by residual: bond pdb=" C GLY A 319 " pdb=" N LEU A 320 " ideal model delta sigma weight residual 1.329 1.279 0.050 1.86e-02 2.89e+03 7.16e+00 bond pdb=" C VAL A 283 " pdb=" N PRO A 284 " ideal model delta sigma weight residual 1.336 1.308 0.028 1.23e-02 6.61e+03 5.19e+00 bond pdb=" C TYR E 495 " pdb=" N GLY E 496 " ideal model delta sigma weight residual 1.332 1.323 0.009 5.00e-03 4.00e+04 3.39e+00 bond pdb=" CA CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sigma weight residual 1.530 1.508 0.022 1.53e-02 4.27e+03 2.13e+00 bond pdb=" CB CYS E 379 " pdb=" SG CYS E 379 " ideal model delta sigma weight residual 1.808 1.760 0.048 3.30e-02 9.18e+02 2.09e+00 ... (remaining 6638 not shown) Histogram of bond angle deviations from ideal: 99.82 - 106.65: 204 106.65 - 113.49: 3595 113.49 - 120.32: 2555 120.32 - 127.16: 2590 127.16 - 133.99: 94 Bond angle restraints: 9038 Sorted by residual: angle pdb=" C PHE E 464 " pdb=" N GLU E 465 " pdb=" CA GLU E 465 " ideal model delta sigma weight residual 122.93 115.46 7.47 1.45e+00 4.76e-01 2.66e+01 angle pdb=" CA CYS E 379 " pdb=" CB CYS E 379 " pdb=" SG CYS E 379 " ideal model delta sigma weight residual 114.40 123.52 -9.12 2.30e+00 1.89e-01 1.57e+01 angle pdb=" N CYS E 379 " pdb=" CA CYS E 379 " pdb=" C CYS E 379 " ideal model delta sigma weight residual 107.88 113.28 -5.40 1.41e+00 5.03e-01 1.47e+01 angle pdb=" CA PHE E 464 " pdb=" C PHE E 464 " pdb=" N GLU E 465 " ideal model delta sigma weight residual 116.21 120.46 -4.25 1.29e+00 6.01e-01 1.09e+01 angle pdb=" C GLN E 409 " pdb=" N ILE E 410 " pdb=" CA ILE E 410 " ideal model delta sigma weight residual 122.59 118.97 3.62 1.10e+00 8.26e-01 1.08e+01 ... (remaining 9033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 3444 17.31 - 34.63: 350 34.63 - 51.94: 72 51.94 - 69.26: 24 69.26 - 86.57: 13 Dihedral angle restraints: 3903 sinusoidal: 1574 harmonic: 2329 Sorted by residual: dihedral pdb=" CB CYS E 391 " pdb=" SG CYS E 391 " pdb=" SG CYS E 525 " pdb=" CB CYS E 525 " ideal model delta sinusoidal sigma weight residual 93.00 10.31 82.69 1 1.00e+01 1.00e-02 8.38e+01 dihedral pdb=" CA VAL E 524 " pdb=" C VAL E 524 " pdb=" N CYS E 525 " pdb=" CA CYS E 525 " ideal model delta harmonic sigma weight residual 180.00 143.31 36.69 0 5.00e+00 4.00e-02 5.38e+01 dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual 93.00 30.17 62.83 1 1.00e+01 1.00e-02 5.22e+01 ... (remaining 3900 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 552 0.035 - 0.071: 286 0.071 - 0.106: 101 0.106 - 0.142: 20 0.142 - 0.177: 3 Chirality restraints: 962 Sorted by residual: chirality pdb=" CA CYS E 379 " pdb=" N CYS E 379 " pdb=" C CYS E 379 " pdb=" CB CYS E 379 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CA ILE A 88 " pdb=" N ILE A 88 " pdb=" C ILE A 88 " pdb=" CB ILE A 88 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CB ILE E 410 " pdb=" CA ILE E 410 " pdb=" CG1 ILE E 410 " pdb=" CG2 ILE E 410 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.54e-01 ... (remaining 959 not shown) Planarity restraints: 1171 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 499 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.13e+00 pdb=" N PRO A 500 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 500 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 500 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 283 " -0.029 5.00e-02 4.00e+02 4.39e-02 3.09e+00 pdb=" N PRO A 284 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 284 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 284 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 473 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.02e+00 pdb=" C TRP A 473 " -0.030 2.00e-02 2.50e+03 pdb=" O TRP A 473 " 0.011 2.00e-02 2.50e+03 pdb=" N MET A 474 " 0.010 2.00e-02 2.50e+03 ... (remaining 1168 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 170 2.63 - 3.20: 6699 3.20 - 3.76: 10796 3.76 - 4.33: 14302 4.33 - 4.90: 21797 Nonbonded interactions: 53764 Sorted by model distance: nonbonded pdb=" O THR A 118 " pdb=" OG1 THR A 122 " model vdw 2.061 2.440 nonbonded pdb=" O ASN A 103 " pdb=" OG SER A 106 " model vdw 2.093 2.440 nonbonded pdb=" OH TYR A 41 " pdb=" OG1 THR E 500 " model vdw 2.138 2.440 nonbonded pdb=" O HIS A 417 " pdb=" OG SER A 420 " model vdw 2.142 2.440 nonbonded pdb=" O THR A 449 " pdb=" OG1 THR A 453 " model vdw 2.157 2.440 ... (remaining 53759 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 4134 2.51 5 N 1063 2.21 5 O 1227 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Write .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.230 Check model and map are aligned: 0.100 Convert atoms to be neutral: 0.060 Process input model: 25.420 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.200 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 35.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.050 6643 Z= 0.414 Angle : 0.836 9.117 9038 Z= 0.486 Chirality : 0.046 0.177 962 Planarity : 0.005 0.044 1166 Dihedral : 15.767 86.573 2390 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 23.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.25), residues: 789 helix: -1.83 (0.22), residues: 385 sheet: -1.82 (0.66), residues: 52 loop : -2.73 (0.28), residues: 352 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.1916 time to fit residues: 48.0372 Evaluate side-chains 132 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.731 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 8.9990 chunk 59 optimal weight: 0.3980 chunk 32 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 31 optimal weight: 0.1980 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 49 ASN ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN A 290 ASN A 338 ASN A 417 HIS A 552 GLN A 556 ASN E 388 ASN ** E 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 481 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 6643 Z= 0.222 Angle : 0.734 9.136 9038 Z= 0.373 Chirality : 0.046 0.307 962 Planarity : 0.005 0.052 1166 Dihedral : 5.605 30.160 893 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 20.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer Outliers : 2.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.28), residues: 789 helix: -0.20 (0.25), residues: 389 sheet: -1.62 (0.67), residues: 52 loop : -1.92 (0.31), residues: 348 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 172 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 182 average time/residue: 0.1702 time to fit residues: 41.6792 Evaluate side-chains 156 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 147 time to evaluate : 0.770 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.0960 time to fit residues: 2.4406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 70 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 63 ASN ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 GLN E 414 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 481 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 6643 Z= 0.238 Angle : 0.723 9.430 9038 Z= 0.361 Chirality : 0.046 0.255 962 Planarity : 0.005 0.047 1166 Dihedral : 5.447 29.236 893 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.29), residues: 789 helix: 0.28 (0.25), residues: 387 sheet: -1.71 (0.62), residues: 60 loop : -1.68 (0.32), residues: 342 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 162 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 167 average time/residue: 0.1754 time to fit residues: 39.1188 Evaluate side-chains 152 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 147 time to evaluate : 0.779 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0740 time to fit residues: 1.6871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 10.0000 chunk 7 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 481 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.089 6643 Z= 0.227 Angle : 0.730 8.997 9038 Z= 0.368 Chirality : 0.044 0.184 962 Planarity : 0.007 0.121 1166 Dihedral : 5.291 29.295 893 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 19.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.29), residues: 789 helix: 0.56 (0.26), residues: 384 sheet: -1.63 (0.65), residues: 60 loop : -1.46 (0.33), residues: 345 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 158 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 162 average time/residue: 0.1829 time to fit residues: 39.6392 Evaluate side-chains 143 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 139 time to evaluate : 0.775 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0690 time to fit residues: 1.5348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 52 optimal weight: 0.0770 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 481 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 6643 Z= 0.242 Angle : 0.721 11.457 9038 Z= 0.363 Chirality : 0.044 0.170 962 Planarity : 0.006 0.113 1166 Dihedral : 5.204 26.893 893 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer Outliers : 2.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.30), residues: 789 helix: 0.63 (0.26), residues: 379 sheet: -1.53 (0.66), residues: 62 loop : -1.40 (0.33), residues: 348 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 155 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 163 average time/residue: 0.1794 time to fit residues: 38.8366 Evaluate side-chains 148 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 140 time to evaluate : 0.755 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0684 time to fit residues: 1.9768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 75 optimal weight: 0.0270 chunk 62 optimal weight: 0.8980 chunk 34 optimal weight: 8.9990 chunk 6 optimal weight: 0.0270 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 72 optimal weight: 0.4980 chunk 8 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 6643 Z= 0.206 Angle : 0.751 11.420 9038 Z= 0.373 Chirality : 0.044 0.174 962 Planarity : 0.005 0.067 1166 Dihedral : 4.913 25.208 893 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.30), residues: 789 helix: 0.68 (0.26), residues: 386 sheet: -0.99 (0.71), residues: 58 loop : -1.29 (0.34), residues: 345 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 153 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 155 average time/residue: 0.1654 time to fit residues: 34.8933 Evaluate side-chains 142 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 141 time to evaluate : 0.759 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0840 time to fit residues: 1.1564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 9.9990 chunk 42 optimal weight: 0.0030 chunk 63 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.096 6643 Z= 0.215 Angle : 0.729 13.814 9038 Z= 0.362 Chirality : 0.045 0.264 962 Planarity : 0.006 0.122 1166 Dihedral : 4.850 24.039 893 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.30), residues: 789 helix: 0.92 (0.27), residues: 385 sheet: -1.01 (0.72), residues: 57 loop : -1.23 (0.34), residues: 347 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 153 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 155 average time/residue: 0.1764 time to fit residues: 36.7526 Evaluate side-chains 146 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 142 time to evaluate : 0.767 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0614 time to fit residues: 1.5120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.4522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 6643 Z= 0.252 Angle : 0.750 11.771 9038 Z= 0.377 Chirality : 0.046 0.230 962 Planarity : 0.006 0.099 1166 Dihedral : 4.958 24.412 893 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.31), residues: 789 helix: 0.94 (0.27), residues: 387 sheet: -1.19 (0.69), residues: 60 loop : -1.15 (0.35), residues: 342 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 145 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 147 average time/residue: 0.1786 time to fit residues: 35.1725 Evaluate side-chains 139 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 136 time to evaluate : 0.826 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0800 time to fit residues: 1.4934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 0.0980 chunk 66 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 325 GLN A 535 HIS E 360 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 6643 Z= 0.270 Angle : 0.788 12.752 9038 Z= 0.391 Chirality : 0.047 0.219 962 Planarity : 0.005 0.054 1166 Dihedral : 5.182 24.874 893 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.31), residues: 789 helix: 0.82 (0.27), residues: 386 sheet: -1.29 (0.69), residues: 60 loop : -1.11 (0.36), residues: 343 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 136 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 138 average time/residue: 0.1739 time to fit residues: 32.3050 Evaluate side-chains 137 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 131 time to evaluate : 0.780 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0715 time to fit residues: 1.8146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.5980 chunk 71 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 49 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.119 6643 Z= 0.258 Angle : 0.799 13.361 9038 Z= 0.397 Chirality : 0.046 0.208 962 Planarity : 0.006 0.129 1166 Dihedral : 5.137 24.346 893 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.31), residues: 789 helix: 0.79 (0.27), residues: 388 sheet: -1.26 (0.70), residues: 60 loop : -1.15 (0.35), residues: 341 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 141 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 143 average time/residue: 0.1871 time to fit residues: 35.8518 Evaluate side-chains 135 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 0.807 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0746 time to fit residues: 1.3486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.9980 chunk 61 optimal weight: 0.1980 chunk 25 optimal weight: 0.0670 chunk 63 optimal weight: 0.0870 chunk 7 optimal weight: 0.2980 chunk 11 optimal weight: 0.0030 chunk 54 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.1306 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 HIS A 552 GLN E 360 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.124046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.105910 restraints weight = 34802.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.110445 restraints weight = 14853.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.113388 restraints weight = 8146.591| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4036 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4036 r_free = 0.4036 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4036 r_free = 0.4036 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4036 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.5159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.650 6643 Z= 0.934 Angle : 0.924 22.254 9038 Z= 0.492 Chirality : 0.049 0.355 962 Planarity : 0.008 0.125 1166 Dihedral : 4.999 23.007 893 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.31), residues: 789 helix: 0.77 (0.27), residues: 388 sheet: -1.34 (0.70), residues: 60 loop : -1.15 (0.35), residues: 341 =============================================================================== Job complete usr+sys time: 1623.72 seconds wall clock time: 30 minutes 13.99 seconds (1813.99 seconds total)